2IFX | pdb_00002ifx

Crystal structure of a putative 4-methylmuconolactone methylisomerase (YP_295714.1) from Ralstonia eutropha JMP134 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2IFX/pdb

• Classification: Structural Genomics/Unknown function
• Organism(s): Cupriavidus necator
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-21 Released: 2006-10-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.202 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Crystal structure of hypothetical protein (YP_295714.1) from Ralstonia Eutropha JMP134 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.49 kDa 
• Atom Count: 1,814 
• Modeled Residue Count: 203 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	114	Cupriavidus necator	Mutation(s): 4  Gene Names: YP_295714.1 EC: 5.4.99.14
UniProt
Find proteins for O51799 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore O51799  Go to UniProtKB:  O51799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.202 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32IFX

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.06	α = 90
b = 46.06	β = 90
c = 124.16	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary